Research workbench
Pntc-aept: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (aep) transaminase from treponema denticola
Analyse Pntc-aept: fusion protein of phosphonate-specific cytidylyltransferase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PD1
- Type
- protein
- Length
- 2,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotidyl TRANSFERASE/AMINOTRANSFERASE, class V
- UniProt
- Q73MU2
- Ligands
- MG, NI, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotidyl TRANSFERASE/AMINOTRANSFERASE, class V | protein | 613 | 38% helix, 21% strand | Q73MU2 |
| B | Nucleotidyl TRANSFERASE/AMINOTRANSFERASE, class V | protein | 607 | 40% helix, 21% strand | Q73MU2 |
| C | Nucleotidyl TRANSFERASE/AMINOTRANSFERASE, class V | protein | 617 | 38% helix, 20% strand | Q73MU2 |
| D | Nucleotidyl TRANSFERASE/AMINOTRANSFERASE, class V | protein | 611 | 39% helix, 21% strand | Q73MU2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · chains C
- SO4 · Sulfate ion · ion · 11 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.86 | 0.88 | 104 | EDO, SO4 |
| 2 | 958 | 0.86 | 0.87 | 123 | empty |
| 3 | 970 | 0.77 | 0.79 | 80 | SO4 |
| 4 | 248 | 0.72 | 0.87 | 33 | SO4, GOL |
| 5 | 101 | 0.71 | 0.93 | 23 | EDO |
Interfaces
3 interfaces between chains.
- B–D · 3147 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3094 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6PD1 · PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q73MU2
- Elsewhere: RCSB PDB 6PD1 · PDBe 6PD1 · UniProt Q73MU2
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